- Author:
- David Nickerson <david.nickerson@gmail.com>
- Date:
- 2021-09-16 00:41:19+12:00
- Desc:
- Updating Noble 1962 model:
* Exposing the membrane potential to the top-level model;
* adding SED-ML for the paced and pacemaker variants of the model.
Using OpenCOR Snapshot release 2021-09-14.
- Permanent Source URI:
- https://models.fieldml.org/workspace/a1/rawfile/f954e59183314cd37f86c8832dc81317d01c8ec5/models/1962_noble/decomposed-n62/1962_noble-freeRunning_interface_model.xml
<?xml version="1.0"?>
<model xmlns="http://www.cellml.org/cellml/1.1#" name="1962_noble-freeRunning_interface_model">
<component name="1962_noble-freeRunning_interface_component">
<variable name="time" private_interface="out" units="ms"/>
<variable name="IStim" private_interface="out" public_interface="in" units="uA_per_mmsq"/>
<variable name="g_K_add" private_interface="out" public_interface="in" units="mS_per_mmsq"/>
<variable name="V" private_interface="in" public_interface="out" units="mV"/>
<variable name="V_initial" private_interface="out" public_interface="in" units="mV"/>
<variable name="Cm" private_interface="out" public_interface="in" units="uF_per_mm2"/>
<variable name="IStimC" private_interface="in" public_interface="out" units="uA_per_mm2"/>
<variable name="i_Na" private_interface="in" public_interface="out" units="uA_per_mm2"/>
<variable name="g_Na_max" private_interface="out" public_interface="in" units="mS_per_mm2"/>
<variable name="g_Na" private_interface="in" public_interface="out" units="mS_per_mm2"/>
<variable name="E_Na" private_interface="out" public_interface="in" units="mV"/>
<variable name="m" private_interface="in" public_interface="out" units="dimensionless"/>
<variable name="m_initial" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="alpha_m" private_interface="in" public_interface="out" units="per_ms"/>
<variable name="beta_m" private_interface="in" public_interface="out" units="per_ms"/>
<variable name="h" private_interface="in" public_interface="out" units="dimensionless"/>
<variable name="h_initial" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="alpha_h" private_interface="in" public_interface="out" units="per_ms"/>
<variable name="beta_h" private_interface="in" public_interface="out" units="per_ms"/>
<variable name="i_K" private_interface="in" public_interface="out" units="uA_per_mm2"/>
<variable name="g_K1" private_interface="in" public_interface="out" units="mS_per_mm2"/>
<variable name="g_K2" private_interface="in" public_interface="out" units="mS_per_mm2"/>
<variable name="n" private_interface="in" public_interface="out" units="dimensionless"/>
<variable name="n_initial" private_interface="out" public_interface="in" units="dimensionless"/>
<variable name="alpha_n" private_interface="in" public_interface="out" units="per_ms"/>
<variable name="beta_n" private_interface="in" public_interface="out" units="per_ms"/>
<variable name="i_Leak" private_interface="in" public_interface="out" units="uA_per_mm2"/>
<variable name="g_L" private_interface="out" public_interface="in" units="mS_per_mm2"/>
<variable name="E_L" private_interface="out" public_interface="in" units="mV"/>
</component>
<group>
<relationship_ref relationship="encapsulation"/>
<component_ref component="1962_noble-freeRunning_interface_component">
<component_ref component="time"/>
<component_ref component="stimulus_protocol"/>
<component_ref component="parameters"/>
<component_ref component="interface"/>
<component_ref component="membrane"/>
<component_ref component="sodium_channel"/>
<component_ref component="sodium_channel_m_gate"/>
<component_ref component="sodium_channel_h_gate"/>
<component_ref component="potassium_channel"/>
<component_ref component="potassium_channel_n_gate"/>
<component_ref component="leakage_current"/>
</component_ref>
</group>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="time_model.xml">
<component component_ref="time" name="time"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="stimulus_protocol_model.xml">
<component component_ref="stimulus_protocol" name="stimulus_protocol"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="parameters_model.xml">
<component component_ref="parameters" name="parameters"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="interface_model.xml">
<component component_ref="interface" name="interface"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="membrane_model.xml">
<component component_ref="membrane" name="membrane"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="sodium_channel_model.xml">
<component component_ref="sodium_channel" name="sodium_channel"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="sodium_channel_m_gate_model.xml">
<component component_ref="sodium_channel_m_gate" name="sodium_channel_m_gate"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="sodium_channel_h_gate_model.xml">
<component component_ref="sodium_channel_h_gate" name="sodium_channel_h_gate"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="potassium_channel_model.xml">
<component component_ref="potassium_channel" name="potassium_channel"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="potassium_channel_n_gate_model.xml">
<component component_ref="potassium_channel_n_gate" name="potassium_channel_n_gate"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="leakage_current_model.xml">
<component component_ref="leakage_current" name="leakage_current"/>
</import>
<import xmlns:xlink="http://www.w3.org/1999/xlink" xlink:href="1962_noble-freeRunning_units_model.xml">
<units name="mm" units_ref="mm"/>
<units name="ng" units_ref="ng"/>
<units name="ms" units_ref="ms"/>
<units name="uA" units_ref="uA"/>
<units name="K" units_ref="K"/>
<units name="nmol" units_ref="nmol"/>
<units name="mmsq" units_ref="mmsq"/>
<units name="mmcu" units_ref="mmcu"/>
<units name="mssq" units_ref="mssq"/>
<units name="mscu" units_ref="mscu"/>
<units name="mV" units_ref="mV"/>
<units name="mVsq" units_ref="mVsq"/>
<units name="mV_per_ms" units_ref="mV_per_ms"/>
<units name="mS" units_ref="mS"/>
<units name="mS_per_mmsq" units_ref="mS_per_mmsq"/>
<units name="mS_per_mm" units_ref="mS_per_mm"/>
<units name="uA_per_mmsq" units_ref="uA_per_mmsq"/>
<units name="uA_per_mmcu" units_ref="uA_per_mmcu"/>
<units name="nC" units_ref="nC"/>
<units name="uF" units_ref="uF"/>
<units name="uF_per_mmsq" units_ref="uF_per_mmsq"/>
<units name="mM" units_ref="mM"/>
<units name="mM_per_ms" units_ref="mM_per_ms"/>
<units name="nN" units_ref="nN"/>
<units name="mPa" units_ref="mPa"/>
<units name="pJ" units_ref="pJ"/>
<units name="nW" units_ref="nW"/>
<units name="per_ms" units_ref="per_ms"/>
<units name="per_mm" units_ref="per_mm"/>
<units name="per_mV" units_ref="per_mV"/>
<units name="per_mV_per_ms" units_ref="per_mV_per_ms"/>
<units name="per_mM_per_ms" units_ref="per_mM_per_ms"/>
<units name="uA_per_mmsq_per_mM" units_ref="uA_per_mmsq_per_mM"/>
<units name="mm_per_ms" units_ref="mm_per_ms"/>
<units name="gas_constant" units_ref="gas_constant"/>
<units name="faradays_constant" units_ref="faradays_constant"/>
<units name="pA_per_pF" units_ref="pA_per_pF"/>
<units name="nS_per_pF" units_ref="nS_per_pF"/>
<units name="uF_per_cmsq" units_ref="uF_per_cmsq"/>
<units name="um" units_ref="um"/>
<units name="umsq" units_ref="umsq"/>
<units name="umcu" units_ref="umcu"/>
<units name="cmcu_per_uF_per_s" units_ref="cmcu_per_uF_per_s"/>
<units name="mM_per_s" units_ref="mM_per_s"/>
<units name="per_mV_ms" units_ref="per_mV_ms"/>
<units name="mS_per_mm2" units_ref="mS_per_mm2"/>
<units name="uF_per_mm2" units_ref="uF_per_mm2"/>
<units name="uA_per_mm2" units_ref="uA_per_mm2"/>
</import>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="time"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="stimulus_protocol"/>
<map_variables variable_1="IStim" variable_2="IStim"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="membrane"/>
<map_variables variable_1="IStim" variable_2="I_stim"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="V_initial" variable_2="V_initial"/>
<map_variables variable_1="Cm" variable_2="Cm"/>
<map_variables variable_1="time" variable_2="time"/>
<map_variables variable_1="IStimC" variable_2="IStimC"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="interface"/>
<map_variables variable_1="IStim" variable_2="I_stim"/>
<map_variables variable_1="g_K_add" variable_2="g_K_add"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="parameters"/>
<map_variables variable_1="g_K_add" variable_2="g_K_add"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="potassium_channel"/>
<map_variables variable_1="g_K_add" variable_2="g_K_add"/>
<map_variables variable_1="i_K" variable_2="i_K"/>
<map_variables variable_1="g_K1" variable_2="g_K1"/>
<map_variables variable_1="g_K2" variable_2="g_K2"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="membrane" component_2="sodium_channel"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="i_Na" variable_2="i_Na"/>
</connection>
<connection>
<map_components component_1="membrane" component_2="sodium_channel_m_gate"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="membrane" component_2="sodium_channel_h_gate"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="membrane" component_2="potassium_channel"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="i_K" variable_2="i_K"/>
</connection>
<connection>
<map_components component_1="membrane" component_2="potassium_channel_n_gate"/>
<map_variables variable_1="V" variable_2="V"/>
</connection>
<connection>
<map_components component_1="membrane" component_2="leakage_current"/>
<map_variables variable_1="V" variable_2="V"/>
<map_variables variable_1="i_Leak" variable_2="i_Leak"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="sodium_channel"/>
<map_variables variable_1="i_Na" variable_2="i_Na"/>
<map_variables variable_1="g_Na_max" variable_2="g_Na_max"/>
<map_variables variable_1="g_Na" variable_2="g_Na"/>
<map_variables variable_1="E_Na" variable_2="E_Na"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="sodium_channel_m_gate"/>
<map_variables variable_1="m" variable_2="m"/>
<map_variables variable_1="m_initial" variable_2="m_initial"/>
<map_variables variable_1="alpha_m" variable_2="alpha_m"/>
<map_variables variable_1="beta_m" variable_2="beta_m"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="sodium_channel_m_gate" component_2="sodium_channel"/>
<map_variables variable_1="m" variable_2="m"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="sodium_channel_h_gate"/>
<map_variables variable_1="h" variable_2="h"/>
<map_variables variable_1="h_initial" variable_2="h_initial"/>
<map_variables variable_1="alpha_h" variable_2="alpha_h"/>
<map_variables variable_1="beta_h" variable_2="beta_h"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="sodium_channel_h_gate" component_2="sodium_channel"/>
<map_variables variable_1="h" variable_2="h"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="potassium_channel_n_gate"/>
<map_variables variable_1="n" variable_2="n"/>
<map_variables variable_1="n_initial" variable_2="n_initial"/>
<map_variables variable_1="alpha_n" variable_2="alpha_n"/>
<map_variables variable_1="beta_n" variable_2="beta_n"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
<connection>
<map_components component_1="potassium_channel_n_gate" component_2="potassium_channel"/>
<map_variables variable_1="n" variable_2="n"/>
</connection>
<connection>
<map_components component_1="1962_noble-freeRunning_interface_component" component_2="leakage_current"/>
<map_variables variable_1="i_Leak" variable_2="i_Leak"/>
<map_variables variable_1="g_L" variable_2="g_L"/>
<map_variables variable_1="E_L" variable_2="E_L"/>
<map_variables variable_1="time" variable_2="time"/>
</connection>
</model>
